Re: base stacking analysis of the trajectory of a nucleic acids simulation

From: Chris Harrison (charris5_at_nd.edu)
Date: Sun Jan 04 2009 - 12:12:07 CST

Look at the programs CURVES or X3DNA, they may be of assistance; however I
don't think they have a "occupancy" definition, or that they handle RNA (in
addition to DNA).

Why not take a similar approach to that in DNA and for a give secondary
structure of RNA define optimal base stacking (as indicated via a local
energy minimum of a PMF where the reaction coordinate is the twisting of the
base out of the "stack") as occupancy 1 and completely orthogonal bases as
occupancy 0, with a range in between labeled for 0.1, 0.2, etc.

C.

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Tue, Dec 30, 2008 at 3:54 PM, Tianjiao Wang <tjwang_at_iastate.edu> wrote:
> Dear all,
>
>  I have finished a molecular dynamics simulation of a small RNA by NAMD
> 2.6.
> I am wondering whether there is a way to quantify the occupancy of base
> stackings between residues from the MD trajectory. Thank you very much for
> your advice and happy holiday!
>
> Tianjiao
>
> Tianjiao Wang
> 3288 MBB
> Iowa State Univ
> Ames, IA 50010
> e-mail: tjwang_at_iastate.edu
>
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